wpa_supplicant.conf would only be used if you managed it yourself and
not via Network-Manager.
It is in the source under nm-device-802-11-wireless.c look for:
const char * ap_scan = "AP_SCAN 1";
HOWEVER, looking over the code it looks like the code is different
than I remember and uses ap_scan 2 when the AP is non-broadcast. You
could try changing that to 1 and see if that helps but the easiest way
to do this would be to create a wpa_supplicant.conf and call it from
wpa_supplicant manually and see if you can associate.